Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 357 bits (917), Expect = e-103 Identities = 201/494 (40%), Positives = 305/494 (61%), Gaps = 14/494 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L +G+ K F GV A+D VDF V EI +L+GENGAGKSTLIK LTGV + DAG + + Sbjct: 12 LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G + +A + I ++QE+NL N++VAEN+FL + +R VD M Sbjct: 72 EGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMR------FGLVDRGAM 125 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 R++ +L G A + + A +Q+V I +A+ +++ +DEPT+SL +E Sbjct: 126 RRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVA 185 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF+++ L+SRGI +VFV+H LD+V + DRI V+R+G+ +GE + E ++ MM+ Sbjct: 186 VLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMML 245 Query: 254 GREVEFFPHGIETRPGEIALEVR----NLKWKDKVKNVS---FEVRKGEVLGFAGLVGAG 306 GRE+E H I + + R + K ++V ++R GEV+G AGL+G+G Sbjct: 246 GRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSG 305 Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366 RTET LVFG+++ + G+ V+G+ V ++ P DAI++G G PEDRK +G+V ++V++N Sbjct: 306 RTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVREN 365 Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426 I+L +L+ W + ++EEI++ +++ L I+TP Q + LSGGNQQK +LA+WL Sbjct: 366 IIL-ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWL 424 Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486 AT +LI DEPTRGIDVGA AEI R+I L A G A++++SSEL EI+ S R+VV+ + Sbjct: 425 ATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRD 484 Query: 487 GEITAVLDNREKRV 500 A L E V Sbjct: 485 RRHVAELRGGEVAV 498 Score = 106 bits (264), Expect = 2e-27 Identities = 66/232 (28%), Positives = 121/232 (52%), Gaps = 6/232 (2%) Query: 29 AVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFK 88 +V+ D ++ E+V L G G+G++ +++ G+ + D GE V+G+ V P DA + Sbjct: 282 SVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIR 341 Query: 89 KGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIG 145 G ++ + ++V ENI LA +A +G R + R + + R LLD+ Sbjct: 342 LGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIP-RCRQEEIADRFIRLLDIRT 400 Query: 146 AKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSR 205 + ++ L+ +Q + + L EPR++ +DEPT + V + +IE L + Sbjct: 401 PH--AEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCAD 458 Query: 206 GISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257 G++++ VS L+E++ S R+VV+RD + + EL+ GE VD I+ + V Sbjct: 459 GMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAIASESV 510 Lambda K H 0.319 0.138 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 657 Number of extensions: 32 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 520 Length of database: 516 Length adjustment: 35 Effective length of query: 485 Effective length of database: 481 Effective search space: 233285 Effective search space used: 233285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory